| --- Log opened Sat Oct 17 00:00:09 2015 | ||
| --- Day changed Sat Oct 17 2015 | ||
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| fenn | delinquentme: it almost sounds like you're trolling when you say things like "i'm writing this verbatim into the patent" | 00:24 |
|---|---|---|
| fenn | anyway, patents are worse than trade secrets because they limit other people | 00:25 |
| fenn | i agree that enzymes are mechanosynthesis | 00:25 |
| fenn | i don't think it's worth anything to try to do DNA mechanosynthesis with an AFM tip | 00:25 |
| fenn | have fun with your patent | 00:25 |
| fenn | try not to rub people's noses in it | 00:27 |
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| delinquentme | nah i was kinda jking just because it would be fun | 00:50 |
| delinquentme | but im with what nmz said | 00:50 |
| delinquentme | fenn, ^ | 00:52 |
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| gene_hacker | it's a bit of a stretch to call enzymes mechanosynthesis | 02:00 |
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| JayDugger | No, he must be over in Mountain View. I've have heard if he'd moved to London. | 04:31 |
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| kanzure | picard maneuver https://www.youtube.com/watch?v=x2o77i74T48 | 05:03 |
| kanzure | gene_hacker is upset because he's busy working on actual mechanosynthesis | 05:04 |
| kanzure | .title http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4322377/ | 05:07 |
| yoleaux | The “Gemini” spinal cord fusion protocol: Reloaded | 05:07 |
| JayDugger | Picard maneuver...that's where everyone pretends an English native sounds French, right? | 05:10 |
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| fenn | bonus points for doing the picard maneuver while simultaneously doing a riker chair straddle http://youtu.be/lVIGhYMwRgs&t=22s | 05:52 |
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| fenn | how about the actual cassini saturn flyby data: http://youtu.be/R2WlXNHaJwY | 06:02 |
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| fenn | http://www.boston.com/bigpicture/2009/04/cassinis_continued_mission.html | 06:44 |
| kanzure | "Swept-source optical coherence tomography powered by a 1.3-μm vertical cavity surface emitting laser enables 2.3-mm-deep brain imaging in mice in vivo" http://biomedicaloptics.spiedigitallibrary.org/article.aspx?articleid=2458790 | 06:46 |
| kanzure | "Native proteins trap high-energy transit conformations" http://advances.sciencemag.org/content/1/9/e1501188.abstract | 06:48 |
| fenn | actually wikipedia has much better versions of those images: https://en.wikipedia.org/wiki/Rings_of_Saturn | 06:49 |
| fenn | some of them | 06:50 |
| kanzure | .ttile http://ambermd.org/ | 06:57 |
| kanzure | .title http://ambermd.org/ | 06:57 |
| yoleaux | The Amber Molecular Dynamics Package | 06:57 |
| kanzure | large email archive too http://archive.ambermd.org/ | 06:58 |
| kanzure | .title http://archive.ambermd.org/201510/0088.html | 06:58 |
| yoleaux | [AMBER] Cytochrome P450 with heme simulation from Abelak, Kavin on 2015-10-09 (Amber Archive Oct 2015) | 06:58 |
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| kanzure | On Sat, Oct 17, 2015 at 1:58 AM, Cathal (Phone) <cathalgarvey@cathalgarvey.me> wrote: | 07:15 |
| kanzure | > If I had time, and if you didn't keep meticulous IRC logs *and* present them | 07:15 |
| kanzure | > for consumption on a public web server, then perhaps I'd take part in HPRM | 07:16 |
| kanzure | > more often. ;) | 07:16 |
| poppingtonic | The Marblestone thesis is a surprisingly good read. Thanks for sharing it, kanzure | 07:26 |
| poppingtonic | Way above my current level of skill, but it feeds the imagination in so many ways. | 07:27 |
| kanzure | which parts are above your "level of skill" in particular? | 07:29 |
| kanzure | and which parts are fascinating | 07:29 |
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| poppingtonic | Anything more intensive than what Church covered in Regenesis covers both. I've been pondering the problem of neural data acquisition - in terms of the kind of information that would be enough to enable whole-brain emulation, and the data that cryonicists hope to store via vitrification. I had considered the possibility of capturing that data at the molecular level, but couldn't think of which techniques could be discussed, because | 07:46 |
| kanzure | cutoff at "discussed, because" | 07:47 |
| poppingtonic | ...continues.. "I don't have the vocabulary yet." | 07:47 |
| poppingtonic | "We structured the analysis around three problems: (1) All neurons must be probed at a sufficient | 07:50 |
| poppingtonic | rate, (2) the energy transmitted into the brain must not cause thermal damage and (3) the volume | 07:50 |
| poppingtonic | of instrumentation introduced into the brain must not cause physical damage. We found that all | 07:50 |
| poppingtonic | existing approaches require orders of magnitude improvement in key parameters in order to scale to | 07:50 |
| poppingtonic | whole brain observations." | 07:50 |
| poppingtonic | " Electrical recording is limited by the low multiplexing capacity of electrodes | 07:50 |
| poppingtonic | and their lack of intrinsic spatial resolution, optical methods are constrained by the scattering of visible | 07:50 |
| poppingtonic | light in brain tissue, magnetic resonance is hindered by the diffusion and relaxation timescales of water | 07:50 |
| poppingtonic | protons, and the implementation of molecular recording is complicated by the stochastic kinetics of | 07:50 |
| poppingtonic | enzymes." | 07:50 |
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| kanzure | smaller brains are easier for whole brain observation | 07:53 |
| poppingtonic | the phrase "stochastic kinetics of enzymes" is interesting. The bigger the brain, the more dimensions you add to an already incredibly high-dimensional space, since every molecule in every synapse has a vector of motion that would need to be captured for accurate state measurement. | 07:57 |
| poppingtonic | .title http://dspace.mit.edu/handle/1721.1/79910 | 08:20 |
| yoleaux | DSpace@MIT: Measuring Cation Dependent DNA Polymerase Fidelity Landscapes by Deep Sequencing | 08:20 |
| poppingtonic | What is misincorporation rate gain? | 08:24 |
| poppingtonic | "We found that Dpo4 acts as a DNA recording device for Manganese with a misincor- | 08:25 |
| poppingtonic | poration rate gain of 2%/mM | 08:25 |
| poppingtonic | " | 08:25 |
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| kanzure | iDavid_: greetings | 09:50 |
| iDavid_ | kanzure: hello :) | 09:56 |
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| kanzure | "ECS is celebrating Open Access Week this year by making all the content—over 120,000 articles—in the ECS Digital Library freely accessible from October 19 through 25, 2015. The ECS Digital Library is home to the Journal of The Electrochemical Society, the flagship journal of ECS, published continuously since 1902, and to the ECS Journal of Solid State Science and Technology, ECS Electrochemistry Letters, ECS Solid State Letters, ... | 11:18 |
| kanzure | ... Electrochemical and Solid-State Letters, ECS Transactions, ECS Meeting Abstracts, and Interface." | 11:18 |
| kanzure | http://www.openaccessweek.org/ | 11:18 |
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| kanzure | http://surgicalneurologyint.com/surgicalint_articles/heaven-the-head-anastomosis-venture-project-outline-for-the-first-human-head-transplantation-with-spinal-linkage-gemini/ | 11:25 |
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| delinquentme | hive mind: mention drexler in a patent ... or no? | 12:13 |
| kanzure | thought you said the patent thing was a joke | 12:19 |
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| delinquentme | kanzure, ohh no i meant that writing the innuendos into the actual patent was a joke | 12:25 |
| delinquentme | the patent is real | 12:25 |
| delinquentme | the pokey tip grazing dehydration and affixing | 12:25 |
| kanzure | "Relative equilibria and the stability of the rings of Saturn" http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.26.5176 | 12:28 |
| kanzure | delinquentme: i don't think it would be good precedent to poach ideas from hplusroadmap and patent everything | 12:29 |
| kanzure | delinquentme: just doesn't seem like a stable strategy to me | 12:29 |
| delinquentme | only patenting those ideas which pertain to the thing im working on | 12:32 |
| delinquentme | I think the central question which needs to be considered here is will i do more good than harm for transhumanisms by patenting this | 12:33 |
| delinquentme | and since none of us happen to be in the vaulted leagues of thiel-esque money yet and funding more hard research | 12:33 |
| delinquentme | i think we need someone to get there | 12:33 |
| delinquentme | in addition if you're contributing ... as stated many times ... you guys have the option to be pulled into this project | 12:34 |
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| delinquentme | - tip chemistry protocols similar to "surface recharing" mentioned by Mann et al ( http://dx.doi.org/10.1166/jctn.2004.008 ) as applied to DNA adhesion to an AFM or STM probe tip | 12:41 |
| delinquentme | i feel like thats WAY too vague | 12:41 |
| delinquentme | thoughts? | 12:41 |
| Whip__ | Nuvigil ? thoughts | 12:42 |
| Whip__ | is it worth the price | 12:42 |
| delinquentme | Whip__, how different from provigil / modafinil | 12:43 |
| delinquentme | i liked my modafinil | 12:43 |
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| Whip__ | delinuentme, it's the new provigil, from what i know is that the patent ranout on provigil and then nuvigil came out | 12:51 |
| Whip__ | i have no experience with either | 12:52 |
| Whip__ | do either of them work or are they just adderall rebranded? | 12:53 |
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| FourFire | ok, so, I just had a rather long talk with the aspiring transhumanist, who calls themselves "Singrana", and am considering reprioritising my goals | 12:59 |
| delinquentme | Whip__, they're def not adderall. | 13:05 |
| delinquentme | much more subtle | 13:05 |
| delinquentme | someting that you could possibly take daily and operate as a good human in society | 13:05 |
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| Whip__ | well thats good the price is pretty outrages though | 13:19 |
| FourFire | topic? | 13:23 |
| mgin | FourFire: reprioritizing how? | 13:23 |
| mgin | hey is anyone here interested in AGI / Strong AI? | 13:23 |
| kanzure | er, yes? | 13:24 |
| poppingtonic | yes | 13:24 |
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| poppingtonic | but to quote Hofstadter, "don't use the term Strong AI - it was invented by John Searle, and you're playing his game" | 13:25 |
| mgin | oh | 13:25 |
| mgin | :) | 13:25 |
| mgin | nice quote | 13:26 |
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| FourFire | mgin consdiering altering my goal reaching strategy | 13:28 |
| FourFire | I'm fearing that I'm wasting far too much time, and I've been reminded, recently that I haven't got very much of it | 13:29 |
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| FourFire | main discussion going on in #lw, channel | 13:29 |
| mgin | sorry i got disconnected | 13:29 |
| FourFire | <FourFire> mgin consdiering altering my goal reaching strategy | 13:30 |
| FourFire | <FourFire> I'm fearing that I'm wasting far too much time, and I've been reminded, recently that I haven't got very much of it | 13:30 |
| FourFire | <FourFire> main discussion going on in #lw, channel | 13:30 |
| mgin | i'm banned from #lesswrong | 13:30 |
| FourFire | hmmh | 13:30 |
| mgin | time anxiety is pretty tough | 13:32 |
| mgin | there's a hard deadline for a hard problem... you have to be very wise and efficient | 13:33 |
| mgin | sometimes that means cutting your losses and changing course... and sometimes it means sticking it out and suffering the anxiety | 13:34 |
| kanzure | FourFire: summary of my comments from #lesswrong to you is that you should give up on a focus on intelligence and instead focus on (cap)ability to make things. intelligence wont build you a bridge or fold your laundry. | 13:36 |
| FourFire | kanzure, I'm not too fussed about intelligence, I know i can't make more, I'm concerned with hacking myself to get higher agency | 13:37 |
| FourFire | and most of all, what to spend it on | 13:37 |
| kanzure | yes but they were telling you "focus on rationalitiessss!!!!!" and i don't think that's possibly helpful in any way.... | 13:38 |
| kanzure | what did singrana say? | 13:38 |
| FourFire | oh I haven't read the responses yet, trying to find a quote | 13:38 |
| kanzure | FourFire: btw, i was once one of the original members of a goal-oriented cult from ~2006 | 13:39 |
| mgin | goal-oriented cult? | 13:39 |
| kanzure | yes, we had a method of brainwashing people into becoming insanely productive goal-obsessed individuals | 13:40 |
| FourFire | ok, I too, have done stupid shit, and thought it was a good idea at the time, but as we live, we encounter more aspects of the world and learn things | 13:40 |
| FourFire | kanzure, you what?? | 13:40 |
| kanzure | thought this was common knowledge around these parts | 13:40 |
| FourFire | describe what this brainwashing involved | 13:40 |
| kanzure | tag teaming | 13:40 |
| FourFire | no, I'm a noob, remember | 13:41 |
| kanzure | like, 14 hour pow-wow sessions just convincing someone of a series of statements and such | 13:41 |
| kanzure | (although, looking back, i think that after 14 hours you can convince anyone of almost anything; but this would have to be more thoroughly tested.) | 13:41 |
| mgin | oh that sounds fun! | 13:41 |
| FourFire | kanzure, quote: the history of mathematics is a history of horrendously difficult problems being solved by young people too ignorant to know that they were impossible. | 13:44 |
| FourFire | (some old high IQ guy that lw people like to quote) | 13:44 |
| kanzure | meh | 13:44 |
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| FourFire | ok, you could say I have calmed down and stopped "freaking out" | 13:55 |
| kanzure | heh, now what was it you were trying to do? life extension? | 13:56 |
| FourFire | (also, please explain how I "freaked out", so I am sure your observations match up with my own) | 13:56 |
| FourFire | were? still am afaik, just uncertain of the best way to go about it | 13:56 |
| kanzure | eh? you're reading too much into "freaked out" | 13:56 |
| mgin | a lot goes into defining one's objective in the first place... | 13:58 |
| kanzure | FourFire: most life extension projects would benefit from far cheaper materials, methods, instruments, tools, etc. | 13:59 |
| kanzure | shouldn't have to be a "one project only" sorta ordeal | 13:59 |
| kanzure | but because of limits of resourcefulness that's what most academics have had to suffer with | 14:00 |
| FourFire | mgin, I want to test my insight from a couple of years back that you can use a(n advanced) genetic algorithm in combination with molecular dynamics software, and an intelligently designed utility function to design protein(s) which perform arbitrary biological functions | 14:00 |
| FourFire | I want to make a tool, which integrates automation of the genetic algorithm, and optimized simulation state backup frequencies, and generation population sizes, and simulation resolution/detail levels, and portability between CPU archetectures | 14:01 |
| FourFire | and use this tool, to design one, maybe two proteins(complexes) | 14:02 |
| kanzure | i am not onvined that there is a way to make a theory that would allow you to design arbitrary protein function, other than bruteforce trial-and-error, and even then that has limitations- the energy necessary to overcome large chasms in state-space is greater than available in the universe in many cases | 14:03 |
| mgin | FourFire: isn't that what you told me you were trying to do last time? | 14:03 |
| kanzure | *onvinced | 14:03 |
| kanzure | *convinced | 14:03 |
| kanzure | you would probably have better results focusing on structural nanotechnology using proteins and peptides | 14:03 |
| FourFire | #1, a mechanism which mimics and/or improves upon and impliments the DNA repair ability of Deinococcus radiodurans, and #2, a custom organelle which can store oxygen at high density inside human cells | 14:03 |
| kanzure | like http://diyhpl.us/~bryan/papers2/bio/protein-engineering/Design%20of%20a%20single-chain%20polypeptide%20tetrahedron%20assembled%20from%20coiled-coil%20segments.pdf | 14:03 |
| FourFire | kanzure, yeah, likely my proof of concept protein (replicate human histone) won't work, and i give up on the whole thing in five years | 14:04 |
| kanzure | an hour in the library an save five years in the lab | 14:05 |
| kanzure | *can save | 14:05 |
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| FourFire | kanzure, so you're telling me that it will definitely not work? | 14:09 |
| kanzure | there are physical forces involved that are still not modeled in molecular dynamics software | 14:10 |
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| kanzure | .title https://www.youtube.com/watch?v=khq7xvzb93c | 14:10 |
| yoleaux | Protein Engineering Webinar - YouTube | 14:10 |
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| kanzure | .title https://www.youtube.com/watch?v=JlASigotkVQ | 14:11 |
| yoleaux | Maureen Hanson - Improving photosynthesis by engineering chloroplast proteins - YouTube | 14:11 |
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| kanzure | .title https://www.youtube.com/watch?v=a6TN-czZY60 | 14:12 |
| yoleaux | Real Vegan Cheese - Engineering yeast to produce casein [cccamp15] - YouTube | 14:12 |
| kanzure | hmm didn't know they did a presentation there | 14:12 |
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| kanzure | .title https://www.youtube.com/watch?v=UTAQYx4f6sc | 14:12 |
| yoleaux | Strategies for Studying Protein-Protein Interactions - YouTube | 14:12 |
| kanzure | .title https://www.youtube.com/watch?v=zP2GhM3cilM | 14:12 |
| yoleaux | Tuning cell-surface receptor signaling through structure-based ligand engineering - YouTube | 14:12 |
| kanzure | ^last one is probably good | 14:12 |
| FourFire | mgin, yes, This is going to take at least 17 years, probably longer, given my proof of concept works | 14:13 |
| FourFire | wow thanks kanzure I know what I'm doing tomorrow, then | 14:14 |
| mgin | that's an extremely long timeline | 14:15 |
| kanzure | .title https://www.youtube.com/watch?v=TUyo8NFi_3Q | 14:15 |
| yoleaux | Intro to Protein Structure Prediction and Design including Review of Protein Structure - YouTube | 14:15 |
| kanzure | .title https://www.youtube.com/watch?v=0E0a5ZaE6Gk | 14:15 |
| yoleaux | George Church on the Future of Human Genomics and Synthetic Biology - YouTube | 14:15 |
| kanzure | there's not many presentations about state-of-the-art in rational protein design, wut | 14:15 |
| kanzure | .title https://www.youtube.com/watch?v=RBPcKbEvK3U | 14:16 |
| yoleaux | 16. Protein Interaction Networks - YouTube | 14:16 |
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| kanzure | .title https://www.youtube.com/watch?v=JX2MdZX6Bys | 14:18 |
| yoleaux | Ron Vale (UCSF) Part 1: Introduction to Motor Proteins - YouTube | 14:18 |
| kanzure | .title https://www.youtube.com/watch?v=yzSgCD7_jSM | 14:18 |
| yoleaux | Mechanics of the kinesin-based transport -- Dr. Wonmuk Hwang - YouTube | 14:18 |
| kanzure | .title https://www.youtube.com/watch?v=ceQ6Kqz8VoY | 14:18 |
| yoleaux | High Speed Protein Simulations with Anton - YouTube | 14:18 |
| kanzure | .title https://www.youtube.com/watch?v=Hz7oHd1mu8k | 14:18 |
| yoleaux | Protein-Protein Docking - YouTube | 14:18 |
| kanzure | .title https://www.youtube.com/watch?v=aJ8WluU7F3Q | 14:20 |
| yoleaux | ChE Capstone Project: Industrial Scale Spider Silk Production - YouTube | 14:20 |
| kanzure | "spiderx" hehe | 14:20 |
| kanzure | ah here we go, how about this one? | 14:21 |
| kanzure | .title https://www.youtube.com/watch?v=F7qjkQZMlIs | 14:21 |
| yoleaux | David Baker - Design of protein structures, functions and assemblies - YouTube | 14:21 |
| kanzure | oh, just foldit stuff. meh. | 14:24 |
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| kanzure | https://www.youtube.com/user/UWfoldit/videos | 14:45 |
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| kanzure | bloop | 19:10 |
| fenn | blorp | 19:11 |
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| fenn | if people want to be exclusive and hold secret meetings that's fine, but apparently i'm never invited to any secret IRC channels with anything important going on | 19:12 |
| fenn | so i have to work in public apparently | 19:12 |
| fenn | or at least that's what i would say if i were trying to cover up my involvement in secret channels | 19:13 |
| kanzure | well done | 19:14 |
| fenn | how's the anonymity working out for you, justanotheruser? | 19:14 |
| kanzure | hm? we know his name | 19:15 |
| fenn | obviously it's "Justan" | 19:15 |
| kanzure | from his github repo | 19:15 |
| fenn | oh poo that's not fun | 19:15 |
| fenn | tbh i'm more worried about crazies like erasmus watching the logs than any patent poachers | 19:16 |
| fenn | we've certainly had enough over the years | 19:17 |
| kanzure | "why should i spill the beans when everyone else is just lurking the logs?" | 19:18 |
| fenn | i could say something like "there are 90blah people lurking and who the hell are they" but actually most of the names on the list are awesome people i know and wish participated here more | 19:20 |
| kanzure | there's a bunch of log lurkers | 19:20 |
| kanzure | not counting the search bots | 19:21 |
| kanzure | since oct11 about 3932 .log requests | 19:21 |
| fenn | wow | 19:21 |
| kanzure | (which does include the search bots) | 19:21 |
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| fenn | how does that compare to random files? | 19:21 |
| kanzure | haven't looked yet. filtering out known bots at the moment. | 19:22 |
| fenn | i wonder if wget -r -c does a lot of requests | 19:23 |
| fenn | even if you've already downloaded the files | 19:23 |
| fenn | /join #project_elrond | 19:25 |
| fenn | abort abort! | 19:25 |
| kanzure | 856 requests when i filter out known-bots | 19:27 |
| kanzure | someone is using page2rss | 19:27 |
| fenn | the smoking gun | 19:28 |
| fenn | it's probably eudoxia | 19:28 |
| kanzure | or yashgaroth or eleitl or any of the other losers | 19:28 |
| kanzure | 217 requests to /logs in that time frame | 19:29 |
| yashgaroth | hey I only check the logs once, maybe 50 times a day, tops | 19:30 |
| kanzure | filthy casual | 19:30 |
| yashgaroth | my money's on eudoxia too, unless he is actually just psychic | 19:31 |
| kanzure | i feel like he would use a user-agent string that proudly rants about lisp | 19:33 |
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| maaku | mgin: you're working on AGI? | 23:03 |
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| maaku | kanzure: for fun, try replacing the logs with markov chain text generated from the actual logs | 23:20 |
| --- Log closed Sun Oct 18 00:00:00 2015 | ||
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